Menu
GeneBe

rs2158177

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000435042.1(TH2LCRR):​n.95-6084T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,202 control chromosomes in the GnomAD database, including 2,539 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2539 hom., cov: 32)

Consequence

TH2LCRR
ENST00000435042.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.461
Variant links:
Genes affected
TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TH2LCRRNR_132125.1 linkuse as main transcriptn.105-6084T>C intron_variant, non_coding_transcript_variant
TH2LCRRNR_132126.1 linkuse as main transcriptn.174+7353T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TH2LCRRENST00000435042.1 linkuse as main transcriptn.95-6084T>C intron_variant, non_coding_transcript_variant 5
TH2LCRRENST00000458509.1 linkuse as main transcriptn.105-6084T>C intron_variant, non_coding_transcript_variant 1
TH2LCRRENST00000417516.1 linkuse as main transcriptn.174+7353T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.177
AC:
26960
AN:
152084
Hom.:
2536
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.214
Gnomad FIN
AF:
0.233
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.177
AC:
26977
AN:
152202
Hom.:
2539
Cov.:
32
AF XY:
0.179
AC XY:
13304
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.220
Gnomad4 EAS
AF:
0.177
Gnomad4 SAS
AF:
0.214
Gnomad4 FIN
AF:
0.233
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.192
Hom.:
528
Bravo
AF:
0.165
Asia WGS
AF:
0.186
AC:
649
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
3.0
DANN
Benign
0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2158177; hg19: chr5-131984058; API